“We are a fit team and I thought we did well and kept on running. We just weren’t good enough,” Jones told reporters.
“I said we wouldn’t use that (tiredness) as an excuse and we are not. Scotland were too good for us in the second half.”
Japan scored the game's first try through Amanaki Mafi, trailed 12-7 at halftime, but the Scots were determined not to go the same way as the Springboks did on Saturday and took control once John Hardie had touched down the first of their five tries.
Despite not blaming tired legs, Jones said the four-day gap between their first two games was not ideal.
"You look at everything involved in rugby and really you need a six-day turnaround. We didn’t get that and you just have to accept it and suck it up. We play a high-energy game, so the boys need a break now.”
Japan's 34-32 win over South Africa reverberated far beyond the game and made headlines around the world, but Jones and captain Michael Leitch were certain their team were not still basking in the glory when they lined-up against Scotland.
"We had to be better today, and that was the challenge," Jones said.
Leitch added: “It was good for the team to come into the game confident. We were pretty hard on not being complacent and fixed any issues approaching Scotland. The result wasn’t one we wanted but we just need to move on.”
Japan now have a long rest before they face Samoa on Oct.3.
“Samoa in 10 days is key. If we knock them off, we will have a fantastic chance," Jones said.
(Reporting by Justin Palmer; Editing by David Goodman)
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